# RNAXPLORER

## NAME

RNAxplorer − manual page for RNAxplorer 0.9.0

## SYNOPSIS

**RNAxplorer**
[*OPTION*]...

## DESCRIPTION

RNAxplorer 0.9.0

The RNAxplorer is a multitool, that offers different sampling and clustering methods to explore RNA energy landscapes.

The RNAxplorer
is a multitool, that offers different methods to explore RNA
energy landscapes. In default mode (or with **−M**
RSH option) it takes an RNA sequence as input (either stdin
or **−−sequence** parameter) and outputs
sampled secondary RNA structures. The repellant sampling
heuristic iteratively penalizes base pairs of local minima
of structures that have been seen too often. This results in
a diverse sample set with the most important low free energy
structures.

Another
important sampling method (**−M** RS option) is
based on reference

structures
(**−−struc1** and
**−−struc2**). This method produces
structures in the vicinity of these two reference
structures. Arbitrary many references can be added if a
fasta file is used as input (via stdin).

Often the output of sampling methods has to be coarse grained by local minima

that are
defined by a gradient walk. A parallelized gradient descent
procedure can be used to retrieve local minima
(**−M** RL option) of sampled structures (input via
stdin). **
−h**,

**−−help**

Print help and exit

**−−detailed−help**

Print help, including all details and hidden options, and exit

**−−full−help**

Print help, including hidden options, and exit

**−V**,
**−−version**

Print version and exit

**General
Options:**

Below are command line options which alter the general behavior of this program

**−v**,
**−−verbose**

Be verbose (default=off)

**Repulsive
Sampling Options:
−−sequence**=

*STRING*

Input sequence (default=‘’)

**−−penalize−structures**

Penalize structures instead of base pairs of local minima, that occure too often. (default=off)

**−−struc1**=*STRING*

Input structure 1 (default=‘’)

**−−struc2**=*STRING*

Input structure 2 (default=‘’)

**−−granularity**=*INT*

Granularity, i.e. number of samples after which distortion checks are performed (default=‘100’)

**−n**,
**−−num−samples**=*INT*

Number of samples in total. The number of samples per iteration is n/g. (default=‘100000’)

**−f**,
**−−exploration−factor**=*FLOAT*

Exploration factor (default=‘1’)

**−−min−exploration−percent**=*FLOAT*

Minimum exploration percentage before adding

new repelled structures

(default=‘1’)

**−−cluster**

Cluster resulting local minima to reduce effective size (default=off)

**−−lmin−file**=*STRING*

Output filename for local minima (default=‘’)

**−−TwoD−file**=*STRING*

Output filename for pseudo−2D file (default=‘’)

**−−nonred**

Do sampling with non−redundant pbacktrack (default=off)

**−−nonred−file**=*STRING*

Input filename for nonredundant samples (default=‘’)

**−2**,
**−−explore−two−neighborhood**

Explore 2−Neighborhood of local minima, i.e.

eliminate shallow minima

(default=off)

**−−post−filter−two**

Post processing Filter local minima according to 2−Neighborhood, i.e. eliminate shallow minima (default=off)

**−−ediff−penalty**

Use energy difference instead of kT for penalty (default=off)

**−−mu**=*FLOAT*

proportion factor used to decide whether sampling round was sufficient (default=‘0.1’)

**Algorithms:**

Select additional algorithms
which should be included in the calculations. Default is the
repellant sampling heuristic. Display more options with
**−−detailed−help**.

**−M**,
**−−method=**<method>

Set the method used to obtain meshpoint structures for the bisection algorithm

(default=‘RSH’)

Available options are:

GW |
Gradient Walk (default) |
|||

MC |
Monte Carlo walk |
|||

MC−SA |
Monte Carlo Walk |

with simulated Annealing

DB−MFE |
Distance based MFE structure |

meshpoints

TRATES |
Transition rate computation | ||

SM |
Stochastic sampling method with 2D mapping (activate distortion |

with
**−e**"N").

RS |
Repellant or Attraction sampling | ||

RSH |
Repellant sampling heuristic | ||

RL |
Retrieve local minima. Standard input should be a sequence and a |

set of secondary structures (one per line). \

**−−betaScale**=*DOUBLE*

Set the scaling of the Boltzmann factors (default=‘1.’)

The argument
provided with this option enables to scale the thermodynamic
temperature used in the Boltzmann factors independently from
the temperature used to scale the individual energy
contributions of the loop types. The Boltzmann factors then
become exp(**−dG**/(kT*betaScale)) where k is the
Boltzmann constant, dG the free energy contribution of the
state and T the absolute temperature.

**−e**,
**−−extended_opt**=*STRING*

Some extended options: N normal distortion (no shift) B alter both potentials at once R relax potential instead of increasing it S shift potential to other structure F shift to first structure V verbose

(default=‘’)

**−i**,
**−−iterations**=*INT*

Set the number of iterations/simulations

(default=‘1’)

**−m**,
**−−maxKeep**=*INT*

maxKeep for direct path search

(default=‘10’)

**−s**,
**−−maxStore**=*INT*

amount of best solutions to hold per iteration

(default=‘10’)

**−r**,
**−−remember**=*INT*

Set the number of structure states to remember in a TABU list

(default=‘10’)

**−c**,
**−−circ**

Assume a circular (instead of linear) RNA molecule.

(default=off)

**−−cooling−rate**=*FLOAT*

Cooling factor used for simulated annealing

(default=‘0.9998’)

**−−tstart**=*FLOAT*

start temperature in deg. Celcius

(default=‘37.0’)

**−−tstop**=*FLOAT*

stop temperature in deg. Celcius

(default=‘0.0’)

**−−penalizeBackWalks**

Add a penalty for backward moves, i.e. moves along states already visited

(default=off)

**−−basinStructure**

just perform a gradient walk starting from a given structure

(default=off)

**−D**,
**−−maxD**=*INT*

Maximum base pair distance between meshpoints and references

(default=‘5’)

**−−maxD1**=*INT*

Maximum base pair distance between meshpoints and reference structure 1

(default=‘5’)

**−−maxD2**=*INT*

Maximum base pair distance between meshpoints and reference structure 2

(default=‘5’)

**Model
Details‘:
−T**,

**−−temp**=

*DOUBLE*

Rescale energy parameters to a temperature of temp C. Default is 37C.

**−−p0**=*STRING*

Set the percentage of the references distortion value <int> to <double> Can be given for all reference indices (NOTE: the value <double> should be between 0 and 1) (example: "−−p0 2=0.5" − distortion value of sequence 2 will be multiplied with 0.5 before sampling.)

**Gradient
walker options‘:
−−shift_moves**

Use shift moves for gradient walks.

(default=off)

**−P**,
**−−parameter_file**=*STRING*

Use the given parameter file for gradient walks.